Contacts of the helix formed by residues 99 - 112 (chain D) in PDB entry 6AHU
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 99 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D PRO 4.7 4.0 - - - -
94D GLN* 3.2 44.4 - - + -
96D TYR* 3.0 24.4 + + + +
98D LEU* 1.3 84.6 - - + +
100D LEU* 1.3 57.1 + - - +
101D PRO 3.5 1.1 - - - -
102D LEU* 3.2 42.4 + - + +
103D HIS 3.4 3.6 + - - -
156D ILE* 3.6 22.4 - - + +
158D LEU* 4.2 20.0 - - + -
168D ILE* 3.7 43.5 - - + -
24K VAL* 5.7 4.3 - - + -
27K GLN* 6.4 0.4 - - + -
28K ASP* 6.3 0.2 - - + -
34K LEU* 4.8 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C GLU* 5.2 10.5 - - - +
96D TYR 3.9 1.8 + - - +
97D SER* 3.4 23.8 + - - +
98D LEU 3.2 0.2 - - - -
99D PHE* 1.3 74.4 - - - +
101D PRO* 1.4 58.0 - - + +
102D LEU 3.2 0.2 - - - -
103D HIS* 3.0 26.7 + - + +
104D GLU* 2.6 40.2 + - + +
156D ILE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C GLN* 4.5 14.4 - - - +
213C GLU* 3.9 36.8 - - + +
97D SER 4.3 2.2 - - - +
98D LEU* 3.3 20.2 - - - +
100D LEU* 1.4 89.8 - - + +
102D LEU* 1.3 58.9 + - - +
104D GLU* 3.6 11.5 - - + +
105D LEU* 2.9 27.5 + - - +
23K CYS* 3.8 22.0 - - - -
27K GLN* 5.5 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU 4.6 4.3 - - - +
99D PHE* 3.2 34.4 + - + +
100D LEU 3.2 0.6 - - - -
101D PRO* 1.3 78.6 - - - +
103D HIS* 1.3 60.4 + - - +
105D LEU* 3.6 7.7 + - + +
106D TRP* 3.3 19.6 + - - +
136D HIS 5.1 0.5 - - - +
137D GLY* 3.9 14.0 - - - +
156D ILE* 5.0 4.7 - - + -
158D LEU* 4.4 17.9 - - + -
16K PHE* 5.2 1.7 - - - -
20K ALA* 4.8 6.1 - - + +
23K CYS* 3.7 27.8 - - + +
24K VAL* 3.8 31.0 - - + -
27K GLN* 6.4 0.4 - - + -
34K LEU* 4.9 1.3 - - + -
38K TYR* 4.3 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D PHE 3.4 4.6 + - - +
100D LEU* 3.0 31.6 + - + +
102D LEU* 1.3 76.6 - - - +
104D GLU* 1.3 63.1 + - - +
106D TRP* 3.4 22.0 + + - +
107D LYS* 2.9 40.8 + - + +
137D GLY 3.5 20.7 + - - +
139D ILE* 3.6 37.6 + - + +
156D ILE* 4.2 15.5 - - + +
187D GLU 5.3 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C GLU* 4.5 21.3 - - + +
214C ASP* 5.4 2.0 - - - -
215C SER* 5.4 2.7 - - - +
100D LEU* 2.6 24.9 + - + +
101D PRO* 3.8 11.9 - - + +
102D LEU 3.3 0.4 - - - -
103D HIS* 1.3 74.2 - - - +
105D LEU* 1.3 62.5 + - - +
107D LYS* 3.7 20.9 + - - +
108D GLN* 3.2 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C SER* 3.4 30.5 - - - +
217C GLU* 4.5 6.0 - - - +
101D PRO 2.9 18.0 + - - +
102D LEU* 3.8 7.6 - - - +
104D GLU* 1.3 78.1 - - - +
106D TRP* 1.3 59.7 + - - +
108D GLN* 3.7 2.0 + - - +
109D TYR* 3.2 21.7 + - - +
16K PHE* 3.7 17.0 - - + -
19K GLN* 3.6 34.5 - - + +
20K ALA* 3.8 38.6 - - + +
23K CYS* 4.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D LEU 3.3 7.4 + - - +
103D HIS* 3.4 31.4 + + - +
104D GLU 3.3 0.2 - - - -
105D LEU* 1.3 77.4 - - - +
107D LYS* 1.3 70.0 + - + +
109D TYR* 3.2 12.4 + + - +
110D ILE* 3.3 48.6 + - + +
130D LEU* 5.3 8.3 - - + +
133D ALA* 6.3 0.8 - - - +
134D ASP 4.1 12.1 + - - -
135D LEU* 4.1 10.8 - - + +
136D HIS 3.9 9.4 - - - +
137D GLY 3.7 17.0 - - - +
138D ALA* 3.7 23.3 - - + -
139D ILE 4.6 1.1 - - - -
186D VAL* 3.6 28.7 - - + -
187D GLU 4.1 15.3 - - - -
188D THR* 5.1 8.1 - - + -
16K PHE* 3.7 28.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D HIS* 2.9 32.5 + - + +
104D GLU* 3.7 25.1 + - - +
105D LEU 3.3 0.6 - - - -
106D TRP* 1.3 85.6 - - + +
108D GLN* 1.3 61.9 + - + +
109D TYR 3.5 0.3 + - - -
110D ILE* 3.7 10.2 + - - +
111D ARG* 3.8 44.3 + - - +
189D ASP* 5.0 12.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ASP* 3.3 22.2 + - - +
215C SER* 3.3 28.6 + - - +
217C GLU* 3.5 17.1 - - - +
104D GLU* 3.2 37.6 + - - +
105D LEU 4.3 2.7 - - - +
107D LYS* 1.3 77.0 - - + +
109D TYR* 1.3 62.2 + - - +
110D ILE 3.4 0.4 - - - -
111D ARG* 3.7 14.5 + - - +
112D ASP* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLU* 5.4 1.6 - - - -
105D LEU* 3.2 18.0 + - + +
106D TRP* 3.2 15.1 + + - +
108D GLN* 1.3 76.7 - - - +
110D ILE* 1.3 79.3 + - + +
112D ASP* 3.3 9.3 + - + +
113D LEU* 3.2 40.1 + - + +
133D ALA* 5.2 5.4 - - + -
134D ASP* 4.6 11.4 - - + -
12K GLN* 3.1 52.3 + - + +
13K ARG* 3.3 22.4 + - + +
15K ASN* 5.1 0.9 - - - -
16K PHE* 3.6 33.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D TRP* 3.3 56.2 + - + +
107D LYS* 3.7 6.0 + - - +
108D GLN 3.4 0.2 - - - -
109D TYR* 1.3 90.1 - - + +
111D ARG* 1.3 65.5 + - + +
113D LEU* 3.2 24.7 + - + +
114D CYS* 3.6 10.5 + - + +
115D SER 4.6 0.2 + - - -
117D LEU* 5.5 9.3 - - + +
126D ILE* 6.3 3.4 - - + -
130D LEU* 4.5 21.3 - - + -
133D ALA* 5.7 1.6 - - + -
188D THR* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LYS* 3.8 37.4 + - - +
108D GLN* 3.7 16.3 + - - +
109D TYR 3.3 0.2 - - - -
110D ILE* 1.3 78.5 - - + +
112D ASP* 1.3 61.9 + - - +
115D SER* 3.4 28.8 - - - +
117D LEU* 4.3 23.3 - - + +
189D ASP* 2.4 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C GLU* 3.0 30.2 - - + +
219C LEU* 5.0 14.8 - - + +
108D GLN* 3.0 19.4 + - - +
109D TYR* 3.3 11.2 + - + +
110D ILE 3.2 0.6 - - - -
111D ARG* 1.3 79.8 - - - +
113D LEU* 1.3 59.8 + - - +
115D SER* 4.8 5.6 - - - -
12K GLN* 5.1 6.2 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il